From Phage Hunting to COVID Variant Sequencing in Southern California Wastewater
Dr. Katrine Whiteson, Professor, University of California Irvine
Video Summary:
Dr. Katrine Whiteson from UC Irvine presented her team's research on wastewater sequencing, particularly during the COVID-19 pandemic. She credited Jason Rothman and his team for their efforts in this shift from their usual focus on the human microbiome to wastewater. The team used sewage samples to hunt for phages, which are viruses that infect bacteria, with the aim of finding alternatives to antibiotics. They had success in identifying phages that target specific pathogens, even from older sewage samples.
During the pandemic, they expanded their research to include RNA sequencing of wastewater to track the presence of viruses, including SARS-CoV-2. They collected samples from eight wastewater treatment plants in Southern California, representing 16 million people. Despite the challenges, such as pasteurizing samples at 70°C, they successfully sequenced RNA and detected various viruses, including tomato viruses which were unexpectedly the most abundant. The team employed both direct RNA sequencing and enrichment methods, including the Illumina respiratory virus panel and Arctic primers, to enhance their analysis. They discovered a high diversity of viral variants, some of which were detected in wastewater before being identified in clinical samples. Whiteson emphasized the importance of considering data that doesn't match existing databases, as there is still much "dark matter" in genomic sequencing, with many unknowns in both human and environmental samples.
Whiteson concluded by encouraging researchers to explore larger databases and use K-mer analysis to better classify unknown sequences. She also highlighted ongoing efforts to improve standards in microbiome research, mentioning collaborations between various organizations to advance the field.